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I use Hotwire and specify 3 people. I haven't done this in NYC, but I have done it elsewhere without a problem. You may pay a little more than the 2 person rate, but it's worth it if you really want 2 beds.

Just be sure to check in in a timely manner. If you're going to arrive late, call the hotel directly late morning on your arrival date and tell them you are definitely coming and to block out a room with 2 beds for you.